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http://technelysium.com.au/?page_id=13

Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Chromas (RRID:SCR_000598) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012c-c7e5-e09d-a061-4a6580000000

Core facility that provides the following services: Flow cytometry assay service, Data management system.

The BD FACSCalibur system combines unique dual-laser technology, an automated sample loader option, and powerful software to provide the high throughput necessary to meet productivity requirements of clinical laboratories. The modularity and innovative technology designed into the BD FACSCalibur system also offers investigators the performance and flexibility required for a variety of research applications. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.

Proper citation: HMS NERCE FACSCalibur Flow Cytometer Resource (RRID:SCR_000879) Copy   

•   Source: SciCrunch Registry

http://web.mit.edu/spectroscopy/facilities/lbrc.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale.

Proper citation: Laser Biomedical Research Center (RRID:SCR_000106) Copy   

•   Source: SciCrunch Registry

https://www.artinis.com/oxysoft

Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements.

Proper citation: Artinis Medical Systems Oxysoft (RRID:SCR_024666) Copy   

•   Source: SciCrunch Registry

https://lifesciences.tecan.com/plate_readers/infinite_200_pro?p=tab--3

Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use.

Proper citation: Tecan i-Control (RRID:SCR_024562) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/cpodes

CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.

Proper citation: CPODES numerical integrator (RRID:SCR_000766) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/StereoCell_v2.0

Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries.

Proper citation: StereoCell v2.0 (RRID:SCR_024438) Copy   

•   Source: SciCrunch Registry

http://www.cma.mgh.harvard.edu/

A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes.

Proper citation: MGH Center for Morphometric Analysis (RRID:SCR_000885) Copy   

•   Source: SciCrunch Registry

https://whonet.org/

Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.

Proper citation: WHONET (RRID:SCR_024495) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/VelvetOptimiser/

Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.

Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy   

•   Source: SciCrunch Registry

https://github.com/EGA-archive/ega-download-client

Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client.

Proper citation: PyEGA (RRID:SCR_024654) Copy   

•   Source: SciCrunch Registry

https://imagetwin.ai/

AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography.

Proper citation: ImageTwin (RRID:SCR_024543) Copy   

•   Source: SciCrunch Registry

https://imagej.net/plugins/3d-imagej-suite/

Software suite provides plugins to enhance 3D capabilities of ImageJ.

Proper citation: 3D ImageJ Suite (RRID:SCR_024534) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssaha2-0

A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Proper citation: Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) Copy   

•   Source: SciCrunch Registry

https://intel.github.io/scikit-learn-intelex/latest/

Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications.

Proper citation: scikit-learn-intelex (RRID:SCR_024595) Copy   

•   Source: SciCrunch Registry

https://github.com/streamlit/streamlit

Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.

Proper citation: streamlit (RRID:SCR_024354) Copy   

•   Source: SciCrunch Registry

http://decgpu.sourceforge.net/homepage.htm

Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.

Proper citation: DecGPU (RRID:SCR_000585) Copy   

•   Source: SciCrunch Registry

https://cme.h-its.org/exelixis/web/software/sweed/

Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.

Proper citation: sweed (RRID:SCR_024357) Copy   

•   Source: SciCrunch Registry

https://www.certara.com/software/phoenix-pkpd/

Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.

Proper citation: WinNonlin (RRID:SCR_024504) Copy   

•   Source: SciCrunch Registry

http://www.paintshoppro.com/en/products/paintshop-pro/standard/

Photo-editing software including editing features, fast brushes, creative tools and color selection that will help turn snapshots into beautiful, gallery-worthy images.

Proper citation: PaintShop Pro (RRID:SCR_000338) Copy   

•   Source: SciCrunch Registry